| Previous changeset 14:3e1f6f6d557e (2023-07-22) Next changeset 16:a79ee60b6926 (2024-02-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit ce8871b2708d391a99cd7656d84eade6f16a1337 |
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modified:
annotateMyIDs.xml |
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| diff -r 3e1f6f6d557e -r cd2480f35935 annotateMyIDs.xml --- a/annotateMyIDs.xml Sat Jul 22 11:14:36 2023 +0000 +++ b/annotateMyIDs.xml Tue Aug 29 22:44:27 2023 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <description>annotate a generic set of identifiers</description> <macros> <token name="@TOOL_VERSION@">3.17.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <xrefs> <xref type="bio.tools">annotatemyids</xref> @@ -15,9 +15,10 @@ <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.rn.eg.db</requirement> <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.at.tair.db</requirement> <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.gg.eg.db</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.bt.eg.db</requirement> </requirements> <version_command><![CDATA[ -echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Rn.eg.db version" $(R --vanilla --slave -e "library(org.Rn.eg.db); cat(sessionInfo()\$otherPkgs\$org.Rn.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ") +echo $(R --version | grep version | grep -v GNU)", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dr.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Dm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Rn.eg.db version" $(R --vanilla --slave -e "library(org.Rn.eg.db); cat(sessionInfo()\$otherPkgs\$org.Rn.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Bt.eg.db version" $(R --vanilla --slave -e "library(org.Bt.eg.db); cat(sessionInfo()\$otherPkgs\$org.Bt.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]></version_command> <command detect_errors="exit_code"><![CDATA[ #if $rscriptOpt: @@ -63,6 +64,9 @@ } else if (organism == "Gg"){ suppressPackageStartupMessages(library(org.Gg.eg.db)) db <- org.Gg.eg.db +} else if (organism == "Bt"){ + suppressPackageStartupMessages(library(org.Bt.eg.db)) + db <- org.Bt.eg.db } else { cat(paste("Organism type not supported", organism)) } @@ -89,6 +93,7 @@ <option value="Dr">Zebrafish</option> <option value="At">Arabidopsis thaliana</option> <option value="Gg">Gallus gallus</option> + <option value="Bt">Bos taurus</option> </param> <param name="id_type" type="select" label="ID Type" help="Select the type of IDs in your input file"> <option value="ENSEMBL" selected="true">Ensembl Gene</option> @@ -198,6 +203,21 @@ </assert_contents> </output> </test> + <!-- Bos taurus database --> + <test expect_num_outputs="1"> + <param name="id_file" value="genelist.txt" ftype="tabular"/> + <param name="id_type" value="SYMBOL"/> + <param name="organism" value="Bt"/> + <param name="output_cols" value="ENSEMBL" /> + <output name="out_tab"> + <assert_contents> + <has_n_columns n="2"/> + <has_n_lines min="9"/> + <has_text_matching expression="ENSBTAG00000007159"/> + <has_text_matching expression="ENSBTAG00000009498"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ |